Genetic analysis of foot-and-mouth disease virus type O isolates responsible for field outbreaks in India between 1993 and 1999

Partial nucleotide sequence at the 3' end of 1D (VP1-encoding) gene of 90 foot-and-mouth disease virus type O isolates recovered from field outbreaks in India between 1993-9 were determined. The sequences were compared with each other and reference viruses. The published sequences of 15 type O isolates recovered from different parts of Asia and one isolate (O1BFS) from Europe and one from Egypt (O1/Sharquia/Egypt/72) were also included in the analysis for comparison. On the basis of phylogenetic analysis the viruses could be grouped into four distinct genotypes (genotypes I-IV). All 90 isolates from India were genotype-I, as were the reference isolates from Bangladesh, China, Egypt, Iran, Saudi Arabia, Syria and Turkey. Genotype-I isolates were further subdivided into 16 sub-genotypes. The Indian isolates were found to be extremely heterogeneous in nature and clustered into 12 different genetic groups. In genotype-I, the nucleotide sequence difference seen between the isolates was 0-11.6%, while among the Indian isolates it is 0-8.8%. Viruses of similar genetic groups are circulating in India, Bangladesh and countries of the Middle East. Genotype-II and -III are represented by isolates from Lebanon(O1/South Lebanon) and Europe (O1-BFS), respectively. Genotype-IV is formed by isolates from China, Hong Kong and Taiwan. The present study reveals the occurrence of viruses belonging to multiple genetic groups over a short period of time and persistence of single genetic group in the same geographical area over several years. This is consistent with the endemic nature of the disease in the country.